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Query Drug-Gene Interactions via Natural Language

Query the Drug Gene Interaction Database (DGIdb) in plain language from Claude Desktop via its public GraphQL API.

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Works with dgidbcloudflare workers
QuentinCody
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91
Spark score
out of 100
Updated 9 days ago
Version 1.0.0
Models
universal
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Why it matters

Access and query the comprehensive Drug-Gene Interaction Database (DGIdb) using natural language through Claude Desktop. This asset allows for seamless integration with DGIdb's GraphQL API, enabling users to retrieve detailed information on drug-gene relationships.

Outcomes

What it gets done

01

Query drug-gene interactions from DGIdb.

02

Retrieve drug attributes and genetic information.

03

Utilize natural language for database queries.

04

Integrate with DGIdb GraphQL API.

Install

Add it to your toolbox

Run in your project directory:

curl -fsSL https://spark.entire.vc/get/vb-dgidb | bash

Overview

DGIdb MCP Server

An MCP server bridging Claude Desktop to the Drug Gene Interaction Database (DGIdb), letting researchers ask plain-language questions about drug-gene interactions answered via DGIdb's public GraphQL API. Use to query drug-gene interaction data conversationally through Claude Desktop. Requires a deployed server instance (typically on Cloudflare Workers) before an end user can connect.

What it does

This MCP server bridges Claude Desktop to the Drug Gene Interaction Database (DGIdb), a comprehensive database aggregating information on how drugs interact with genes from many source databases. Once connected, it lets a researcher ask plain-language questions - "What are the interactions for the drug Imatinib?", "Find genes that interact with Dovitinib", "Show me drug attributes for Trametinib" - and Claude uses the server to query DGIdb and present the results directly. Under the hood, the server calls DGIdb's publicly available GraphQL API at https://dgidb.org/api/graphql. "MCP" stands for Model Context Protocol - the mechanism that lets an AI model like the one in Claude Desktop call external tools - and this server is the piece of software that implements that bridge specifically for DGIdb, giving Claude the "tool" it needs to look information up in the database rather than relying only on its own training knowledge.

When to use - and when NOT to

Use this when a scientist or researcher wants to look up drug-gene interaction data conversationally through Claude Desktop rather than querying DGIdb's API or web interface directly. It requires a deployed instance of the server (typically set up by a technical colleague on Cloudflare Workers) before an end user can connect to it - this connector alone doesn't provide a hosted endpoint.

Capabilities

Answers questions about drug-gene interactions and drug attributes by querying DGIdb's GraphQL API, surfacing the results in plain language within a Claude Desktop conversation.

How to install

An end user adds the server to their Claude Desktop configuration file, under mcpServers, using mcp-remote pointed at the deployed server's URL:

{
  "mcpServers": {
    "dgidb": {
      "command": "npx",
      "args": [
        "mcp-remote",
        "https://dgidb-mcp-server.quentincody.workers.dev/mcp"
      ]
    }
  }
}

The URL shown is illustrative - it must be replaced with the actual address of your own deployed instance, and Claude Desktop needs a restart after the configuration change for it to take effect. For technical users deploying their own instance, the server runs on Cloudflare Workers (via npm create cloudflare@latest), with the connection and tool logic defined in src/index.ts; once deployed, the same server can also be reached from other MCP clients such as the Cloudflare AI Playground by pointing them at its URL. The project is available under the MIT License with an added Academic Citation Requirement: academic or scientific publications using this software must cite it per CITATION.md, while commercial and non-academic use follows standard MIT terms with no citation requirement.

Who it's for

Scientists and researchers who want to query drug-gene interaction data conversationally through Claude Desktop, and the technical users who deploy and maintain the underlying Cloudflare Workers instance for them.

Source README

Interacting with the Drug Gene Interaction Database (DGIdb) via Claude Desktop

What is this?

  • DGIdb: A comprehensive database containing information about how drugs interact with genes. It gathers data from many different sources.
  • MCP Server: A piece of software that acts as a bridge. This specific server connects to the DGIdb API. "MCP" stands for Model Context Protocol, a way for AI models (like the one in Claude) to use tools.
  • Claude Desktop: An application where you can interact with an AI assistant. By configuring it correctly, Claude can use this MCP Server to fetch data from DGIdb for you.

Essentially, this server gives Claude the "tool" it needs to look up information in the DGIdb.

How to Use This with Claude Desktop

If this DGIdb MCP Server has been set up and deployed (e.g., by a technical colleague), you can connect your Claude Desktop application to it. This allows you to ask Claude questions like:

  • "What are the interactions for the drug Imatinib?"
  • "Find genes that interact with Dovitinib."
  • "Show me drug attributes for Trametinib."

Claude will then use this server to find the answers in the DGIdb and present them to you.

Configuration for Claude Desktop

Your Claude Desktop application needs to be told where to find this DGIdb server. This is usually done by editing a configuration file for Claude Desktop.

A technical user or administrator would typically handle the deployment of the server and provide you with a specific URL (web address). For example, the server might be available at an address like: https://dgidb-mcp-server.your-organization.workers.dev/mcp.

The configuration in Claude Desktop would then look something like this. You would add the "dgidb" section within the mcpServers part of your Claude Desktop configuration file:

{
  "mcpServers": {
    // ... (other server configurations might be here) ...

    "dgidb": {
      "command": "npx",
      "args": [
        "mcp-remote",
        "https://dgidb-mcp-server.quentincody.workers.dev/mcp" // <-- This URL needs to be the actual address of YOUR deployed DGIdb MCP server
      ]
    }

    // ... (other server configurations might be here) ...
  }
}

Important:

  • The URL https://dgidb-mcp-server.quentincody.workers.dev/mcp in the example above is illustrative. You will need to replace it with the actual URL where your instance of the DGIdb MCP server is running.
  • After updating the configuration, you usually need to restart Claude Desktop for the changes to take effect.

Once configured, the DGIdb tool should become available within Claude, allowing you to query the database easily.

For Technical Users: Deploying the Server

If you are a technical user and need to deploy this server (e.g., on Cloudflare Workers):

  1. Get Started:
    You can deploy this server to Cloudflare Workers. Refer to the original, more technical README for deployment buttons and command-line instructions (often involving npm create cloudflare@latest).

  2. Customization:
    The server code is in src/index.ts. This file defines how the server connects to DGIdb and what "tools" it provides to MCP clients.

  3. Connecting to Other Clients (like AI Playground):
    Once deployed, you can also connect to your MCP server from other clients like the Cloudflare AI Playground by providing its URL (e.g., https://your-dgidb-server-name.your-account.workers.dev/mcp).

This DGIdb MCP Server uses the publicly available DGIdb GraphQL API at https://dgidb.org/api/graphql.

FAQ

Common questions

Discussion

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